A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2025-04-18, 11:01 UTC
based on data in:
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant.URL: https://github.com/bigbio/pmultiqc
Experimental Design
This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.
You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html
| Sample Name | MSstats_Condition | MSstats_BioReplicate | Fraction_Group | Fraction | Label |
|---|---|---|---|---|---|
| 1 | CT=Mixture;CN=UPS1;QY=0.1fmol | 1 | |||
1 | 1 | 1 | |||
2 | 1 | 1 | |||
| 2 | CT=Mixture;CN=UPS1;QY=0.25fmol | 2 | |||
3 | 1 | 1 | |||
4 | 1 | 1 |
Summary Table
This table shows the quantms pipeline summary statistics.
This table shows the quantms pipeline summary statistics.
| #Peptides Quantified | #Proteins Quantified |
|---|---|
| 5729 | 1605 |
Pipeline Result Statistics
This plot shows the quantms pipeline final result.
Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、
and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained
from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.
| Sample Name | MSstats_Condition | Fraction | #Peptide IDs | #Unambiguous Peptide IDs | #Modified Peptide IDs | #Protein (group) IDs |
|---|---|---|---|---|---|---|
| 1 | CT=Mixture;CN=UPS1;QY=0.1fmol | |||||
1 | 5407 | 5407 | 871 | 1552 | ||
1 | 5434 | 5434 | 880 | 1562 | ||
| 2 | CT=Mixture;CN=UPS1;QY=0.25fmol | |||||
1 | 5572 | 5572 | 901 | 1578 | ||
1 | 5558 | 5558 | 896 | 1588 |
Number of Peptides identified Per Protein
This plot shows the number of peptides per protein in quantms pipeline final result
This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.
Peptides Quantification Table
This plot shows the quantification information of peptides in the final result (mainly the mzTab file).
The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.
- BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
- Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
- Peptide intensity in each condition (Eg.
CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately.
| PeptideID | Protein Name | Peptide Sequence | Best Search Score | Average Intensity | CT=Mixture;CN=UPS1;QY=0.1fmol | CT=Mixture;CN=UPS1;QY=0.25fmol |
|---|---|---|---|---|---|---|
| 1 | TOLA_ECOLI | AAAEADDIFGELSSGK | 1.0000 | 5.9278 | 5.8889 | 5.9636 |
| 2 | G3P2_ECOLI | AAAENIIPHTTGAAK | 1.0000 | 5.8269 | 5.7804 | 5.8688 |
| 3 | RLMH_ECOLI | AAAEQSWSLSALTLPHPLVR | 1.0000 | 6.2390 | 6.1953 | 6.2787 |
| 4 | PDXJ_ECOLI | AAAEVGAPFIEIHTGCYADAK | 0.9997 | 5.4008 | 5.4976 | 5.2760 |
| 5 | RL10_ECOLI | AAAFEGELIPASQIDR | 1.0000 | 8.2489 | 8.2045 | 8.2892 |
| 6 | YFGM_ECOLI | AAAQLQQGLADTSDENLK | 1.0000 | 6.3880 | 6.3969 | 6.3789 |
| 7 | YFGM_ECOLI | AAAQLQQGLADTSDENLKAVINLR | 1.0000 | 6.1712 | 6.0321 | 6.2764 |
| 8 | RHLE_ECOLI | AAATGEALSLVCVDEHK | 1.0000 | 5.7073 | 5.6799 | 5.7331 |
| 9 | SYP_ECOLI | AAATQEMTLVDTPNAK | 1.0000 | 6.2840 | 6.2035 | 6.3518 |
| 10 | EUTL_ECOLI | AACNAFTDAVLEIAR | 1.0000 | 5.6299 | 5.6044 | 5.6541 |
| 11 | ACRB_ECOLI | AADGQMVPFSAFSSSR | 1.0000 | 6.0764 | 5.9387 | 6.1808 |
| 12 | YIDA_ECOLI | AADGSTVAQTALSYDDYR | 0.9998 | 5.6988 | 5.6826 | 5.7144 |
| 13 | ADHE_ECOLI | AADIVLQAAIAAGAPK | 1.0000 | 7.3764 | 7.3461 | 7.4048 |
| 14 | NARG_ECOLI | AADLVDALGQENNPEWK | 1.0000 | 5.6929 | 5.6454 | 5.7357 |
| 15 | DNAK_ECOLI | AADNKSLGQFNLDGINPAPR | 0.9998 | 5.5334 | 5.4957 | 5.5510 |
| 16 | OXYR_ECOLI | AADSCHVSQPTLSGQIR | 1.0000 | 6.2817 | 6.2485 | 6.3126 |
| 17 | TALA_ECOLI | AAEELEKEGINCNLTLLFSFAQAR | 1.0000 | 6.2640 | 6.2059 | 6.3153 |
| 18 | HEMY_ECOLI | AAELAGNDTIPVEITR | 0.9999 | 6.4392 | 6.4256 | 6.4523 |
| 19 | SYL_ECOLI | AAENNPELAAFIDECR | 1.0000 | 6.6836 | 6.6402 | 6.7231 |
| 20 | TALB_ECOLI | AAEQLEKEGINCNLTLLFSFAQAR | 1.0000 | 6.9806 | 6.8963 | 7.0512 |
| 21 | MBHM_ECOLI | AAESALNIDVPVNAQYIR | 1.0000 | 6.1335 | 6.1304 | 6.1366 |
| 22 | DNAG_ECOLI | AAESGVSRPVPQLKR | 0.9999 | 5.1143 | 4.9585 | 5.2288 |
| 23 | HDFR_ECOLI | AAESLYLTQSAVSFR | 1.0000 | 5.7540 | 5.7105 | 5.7935 |
| 24 | RNE_ECOLI | AAESRPAPFLIHQESNVIVR | 1.0000 | 6.5752 | 6.5572 | 6.5925 |
| 25 | HFLK_ECOLI | AAFDDAIAARENEQQYIR | 1.0000 | 5.8013 | 5.6354 | 5.9210 |
| 26 | AROF_ECOLI | AAFPLSLQQEAQIADSR | 1.0000 | 5.9273 | 5.9306 | 5.9241 |
| 27 | AROF_ECOLI | AAFPLSLQQEAQIADSRK | 0.9998 | 5.7612 | 5.7318 | 5.7887 |
| 28 | BOLA_ECOLI | AAFQPVFLEVVDESYR | 1.0000 | 6.4279 | 6.4107 | 6.4444 |
| 29 | CLPB_ECOLI | AAGATTANITQAIEQMR | 1.0000 | 5.9836 | 5.9726 | 5.9908 |
| 30 | YBIS_ECOLI | AAGEPLPAVVPAGPDNPMGLYALYIGR | 1.0000 | 5.9628 | 5.8381 | 6.0596 |
| 31 | SDHA_ECOLI | AAGLHLQESIAEQGALR | 1.0000 | 5.4225 | 5.4295 | 5.4154 |
| 32 | TALA_ECOLI | AAGLSQYEHLIDDAIAWGK | 0.9998 | 5.1833 | 5.1162 | 5.2413 |
| 33 | TALA_ECOLI | AAGLSQYEHLIDDAIAWGKK | 1.0000 | 5.8222 | 5.7763 | 5.8638 |
| 34 | ADHE_ECOLI | AAGVETEVFFEVEADPTLSIVR | 1.0000 | 6.4683 | 6.5168 | 6.4137 |
| 35 | ADHE_ECOLI | AAGVETEVFFEVEADPTLSIVRK | 0.9998 | 6.8321 | 6.7758 | 6.8819 |
| 36 | ENO_ECOLI | AAGYELGKDITLAMDCAASEFYK | 1.0000 | 6.6467 | 6.6291 | 6.6636 |
| 37 | YEBE_ECOLI | AAHQDEPQFGAQSTPLDER | 0.9998 | 5.6491 | 5.6220 | 5.6746 |
| 38 | RIBB_ECOLI | AAIADGAKPSDLNRPGHVFPLR | 1.0000 | 6.4630 | 6.4313 | 6.4926 |
| 39 | DEOC_ECOLI | AAIAYGADEVDVVFPYR | 1.0000 | 6.7499 | 6.6917 | 6.8012 |
| 40 | IDH_ECOLI | AAIEYAIANDRDSVTLVHK | 1.0000 | 6.2872 | 6.2689 | 6.3048 |
| 41 | DPO1_ECOLI | AAINAPMQGTAADIIKR | 0.9998 | 5.8750 | 5.8517 | 5.8972 |
| 42 | SYFA_ECOLI | AAISQASDVAALDNVR | 1.0000 | 6.5821 | 6.5777 | 6.5864 |
| 43 | SYFA_ECOLI | AAISQASDVAALDNVRVEYLGK | 1.0000 | 6.0451 | 5.9836 | 6.0990 |
| 44 | MUKF_ECOLI | AAISSCELLLSETSGTLR | 0.9998 | 5.4539 | 5.3950 | 5.5057 |
| 45 | MSCM_ECOLI | AAKPAQPEVVEALQSALNALEER | 0.9999 | 5.2647 | 5.1693 | 5.3428 |
| 46 | AMPN_ECOLI | AALEQLKGLENLSGDLYEK | 1.0000 | 6.2583 | 6.1947 | 6.3138 |
| 47 | DBHA_ECOLI | AALESTLAAITESLK | 1.0000 | 7.0020 | 7.0119 | 6.9919 |
| 48 | HEM3_ECOLI | AALPPEISLPAVGQGAVGIECR | 0.9999 | 6.3107 | 6.2797 | 6.3396 |
| 49 | SDHA_ECOLI | AALQISQSGQTCALLSK | 0.9999 | 5.5633 | 5.4781 | 5.6344 |
| 50 | DHE4_ECOLI | AANAGGVATSGLEMAQNAAR | 1.0000 | 5.7321 | 5.6606 | 5.7934 |
Protein Quantification Table
This plot shows the quantification information of proteins in the final result (mainly the mzTab file).
The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.
- Peptides_Number: The number of peptides for each protein.
- Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
- Protein intensity in each condition (Eg.
CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.
| ProteinID | Protein Name | Number of Peptides | Average Intensity | CT=Mixture;CN=UPS1;QY=0.1fmol | CT=Mixture;CN=UPS1;QY=0.25fmol |
|---|---|---|---|---|---|
| 1 | 3PASE_ECOLI | 1 | 5.6235 | 5.6046 | 5.6415 |
| 2 | 5DNU_ECOLI | 1 | 5.1934 | 5.1118 | 5.2621 |
| 3 | 6PGD_ECOLI | 10 | 7.4306 | 7.4143 | 7.4446 |
| 4 | 6PGL_ECOLI | 2 | 6.5057 | 6.4721 | 6.5331 |
| 5 | AAEB_ECOLI | 1 | 6.1800 | 6.1410 | 6.2158 |
| 6 | AAS_ECOLI | 4 | 6.0912 | 6.0728 | 6.0645 |
| 7 | AAT_ECOLI | 2 | 7.1735 | 7.1515 | 7.1944 |
| 8 | ABGT_ECOLI | 1 | 5.2444 | 5.3301 | 5.1374 |
| 9 | ACCA_ECOLI | 10 | 7.5188 | 7.4724 | 7.5607 |
| 10 | ACCC_ECOLI | 11 | 7.5447 | 7.5080 | 7.5786 |
| 11 | ACCD_ECOLI | 4 | 6.9568 | 6.9438 | 6.9695 |
| 12 | ACEA_ECOLI | 10 | 7.0495 | 7.0004 | 7.0936 |
| 13 | ACFD_ECOLI | 8 | 6.8296 | 6.7905 | 6.8657 |
| 14 | ACKA_ECOLI | 9 | 8.1525 | 8.1204 | 8.1816 |
| 15 | ACNA_ECOLI | 5 | 6.1236 | 6.0315 | 6.1795 |
| 16 | ACNB_ECOLI | 11 | 7.4528 | 7.4149 | 7.4828 |
| 17 | ACRA_ECOLI | 6 | 7.4974 | 7.4509 | 7.5394 |
| 18 | ACRB_ECOLI | 6 | 6.7660 | 6.6959 | 6.8263 |
| 19 | ACSA_ECOLI | 2 | 5.6039 | 5.6355 | 5.5511 |
| 20 | ACUI_ECOLI | 5 | 7.0524 | 6.9583 | 7.1097 |
| 21 | ACYP_ECOLI | 1 | 5.6173 | 5.6039 | 5.6238 |
| 22 | ADD_ECOLI | 5 | 7.1199 | 7.1375 | 7.1068 |
| 23 | ADEC_ECOLI | 1 | 5.3880 | 5.3527 | 5.4207 |
| 24 | ADHE_ECOLI | 33 | 8.5391 | 8.4942 | 8.5798 |
| 25 | ADHP_ECOLI | 2 | 5.8313 | 5.8293 | 5.8333 |
| 26 | ADIA_ECOLI | 3 | 5.9251 | 5.8502 | 5.9848 |
| 27 | ADPP_ECOLI | 2 | 6.3923 | 6.3622 | 6.4204 |
| 28 | AGP_ECOLI | 3 | 6.1377 | 6.1064 | 6.1668 |
| 29 | AHPC_ECOLI | 9 | 7.9186 | 7.8892 | 7.9463 |
| 30 | AHPF_ECOLI | 9 | 7.4292 | 7.4037 | 7.4533 |
| 31 | AHR_ECOLI | 1 | 5.0382 | 5.1352 | 4.9801 |
| 32 | AK1H_ECOLI | 7 | 6.4884 | 6.4593 | 6.5158 |
| 33 | AK2H_ECOLI | 4 | 6.5019 | 6.4721 | 6.5298 |
| 34 | AK3_ECOLI | 5 | 6.6134 | 6.5366 | 6.6421 |
| 35 | ALAA_ECOLI | 3 | 6.6067 | 6.5814 | 6.6305 |
| 36 | ALAC_ECOLI | 5 | 6.4739 | 6.4394 | 6.5059 |
| 37 | ALDB_ECOLI | 1 | 6.0428 | 6.0105 | 6.0729 |
| 38 | ALF1_ECOLI | 2 | 5.7993 | 5.0883 | 5.8061 |
| 39 | ALF_ECOLI | 10 | 7.9717 | 7.9422 | 7.9992 |
| 40 | ALKH_ECOLI | 3 | 6.6459 | 6.5686 | 6.7115 |
| 41 | ALR1_ECOLI | 3 | 6.6652 | 6.6304 | 6.6974 |
| 42 | AMIA_ECOLI | 1 | 5.8082 | 5.7658 | 5.8469 |
| 43 | AMIB_ECOLI | 2 | 5.7290 | 5.6933 | 5.7621 |
| 44 | AMIC_ECOLI | 5 | 5.9764 | 5.8423 | 6.0306 |
| 45 | AMID_ECOLI | 1 | 4.6107 | 4.3583 | 4.6972 |
| 46 | AMN_ECOLI | 8 | 6.7648 | 6.7423 | 6.7877 |
| 47 | AMPA_ECOLI | 7 | 7.1145 | 7.0752 | 7.1505 |
| 48 | AMPC_ECOLI | 2 | 6.1201 | 6.0621 | 6.1713 |
| 49 | AMPH_ECOLI | 2 | 6.1563 | 6.0922 | 6.2121 |
| 50 | AMPN_ECOLI | 7 | 7.0764 | 7.0526 | 7.0991 |
nf-core/quantms Software Versions
nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms
| Process Name | Software | Version |
|---|---|---|
| ASSEMBLE_EMPIRICAL_LIBRARY | DIA-NN | 1.8.1 |
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.5 |
| yaml | 5.4.1 | |
| DIANNCFG | sdrf-pipelines | 0.0.21 |
| DIANNCONVERT | sdrf-pipelines | 0.0.21 |
| DIANNSUMMARY | DIA-NN | 1.8.1 |
| DIANN_PRELIMINARY_ANALYSIS | DIA-NN | 1.8.1 |
| INDIVIDUAL_FINAL_ANALYSIS | DIA-NN | 1.8.1 |
| MSSTATS | bioconductor-msstats | 4.2.0 |
| r-base | 4.1.2 | |
| SAMPLESHEET_CHECK | sdrf-pipelines | 0.0.21 |
| SDRFPARSING | sdrf-pipelines | 0.0.21 |
| THERMORAWFILEPARSER | ThermoRawFileParser | 1.3.4 |
| Workflow | Nextflow | 21.10.6 |
| nf-core/quantms | 1.1dev |
nf-core/quantms Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms
Core Nextflow options
- runName
- voluminous_thompson
- containerEngine
- docker
- launchDir
- /home/chengxin/newPR/quantms
- workDir
- /home/chengxin/newPR/quantms/work
- projectDir
- /home/chengxin/newPR/quantms
- userName
- chengxin
- profile
- test_dia,docker
- configFiles
- /home/chengxin/newPR/quantms/nextflow.config
Input/output options
- input
- /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
- outdir
- ./results_dia
Protein database
- database
- /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta
Database search
- allowed_missed_cleavages
- 1
- instrument
- N/A
- max_precursor_charge
- 3
- min_peptide_length
- 15
- max_peptide_length
- 30
- max_mods
- 2
Modification localization
- luciphor_debug
- N/A
PSM re-scoring (general)
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- N/A
Consensus ID
- consensusid_considered_top_hits
- N/A
- min_consensus_support
- N/A
Isobaric analyzer
- select_activation
- HCD
Protein Quantification (DDA)
- ratios
- N/A
- normalize
- N/A
- fix_peptides
- N/A
DIA-NN
- acquisition_method
- N/A
- mass_acc_ms2
- 13
- mass_acc_ms1
- 7
- scan_window
- 8
- min_pr_mz
- 350
- max_pr_mz
- 950
- min_fr_mz
- 500
- max_fr_mz
- 1500
- diann_normalize
- N/A
Statistical post-processing
- contrasts
- pairwise
Quality control
- enable_pmultiqc
- true
Institutional config options
- config_profile_name
- Test profile for DIA
- config_profile_description
- Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.
Max job request options
- max_cpus
- 2
- max_memory
- 6 GB
- max_time
- 2d
Generic options
- hostnames
- N/A
